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There is provided an apparatus for analyzing a biomaterial. The apparatus includes: a first substrate including a plurality of micro-pillars formed to protrude to a predetermined height, the biomaterial being attached to one surface of the micro-pillar; a second substrate including a plurality of micro-wells, the micro-pillars being insertable into the micro-wells when the first substrate-and the second substrate are combined with each other; and at least one spacer disposed between the first substrate and the second substrate when the first substrate and the second substrate are combined with each other.